[ccp4bb] Phoenix crystallisation robot
Dear all, We are looking for someone to take over our Art Robins Phoenix crystallisation robot, including the base module with 96 syringe head, wash module, nano module and humidifier chamber. The robot was purchased in 2008 and is in perfect condition. Please contact me for more information. Price to be discussed. Kind regards, Inge Dr. Inge Van Molle VIB Structural Biology Research Center Structural Biology Brussels Vrije Universiteit Brussel Building E, Pleinlaan 2, 1050 Brussel, Belgium Tel 003226291859 Mobile 0032486521278
[ccp4bb] PhD position in structure-function studies of redox stress signaling proteins
On behalf of Prof Joris Messens: PhD position in structure-function studies of redox stress signaling proteinsPosition: A PhD Research position is immediately available for structure-function studies on peroxiredoxins of pathogentic Actinomycetes that control signaling during oxidative stress. Successful candidates will join an exciting research environment of the Messens VIB-laboratory in the Structural Biology Research Center in Brussels. The Messens laboratory is recognized as a world leader in the redox field, and the lab provides an outstanding position in protein biochemistry and structure, in a highly dynamic and team-oriented research group. Successful candidates will work on the FWO-project ‘A Combined Experimental and Theoretical Approach towards Sulfenylation in the Peroxiredoxin AhpE of M. tuberculosis: Unraveling its Redox Chemistry’ in collaboration with the Frank De Proft lab at the VUB, specialized in quantum chemical calculations, and with the Madia Trujillo lab at Universidad de la República Uruguay. In this cutting-edge research environment, you will tackle essential biological problems in oxidative stress signaling and redox regulation.Project: Every 20 seconds a person dies from tuberculosis (TB), which sums up to over 2 million deaths each year. Therefore, the World Health Organization as well as the European Commission consider fighting TB as one of the main goals for the coming years. The agent causing TB is Mycobacterium tuberculosis (Mtb). Mtb infects, resides and multiplies in alveolar macrophages. Mtb causes the formation of granulomas, where this pathogen is exposed to reactive oxygen species (ROS) and reactive nitrogen species, which generate a toxic environment aimed to kill the bacteria. Mtb engages advanced strategies to fight oxidative stress. One of the key enzymes in the defence mechanism of Mtb is the one-cys peroxiredoxin AhpE. AhpE scavenges ROS by its active site cysteine. In this process, the cysteine is oxidized to the sulfenic acid. We will study how the enzymatic environment influences the cysteine sulfenylation, and the electron-transfer pathways in which AhpE is involved. We will use a multidisciplinary approach involving structural and kinetic experiments, and theoretical calculations to establish the rate determining structural environment for cysteine sulfenylation. The moment we understand the details of this ROS-scavenging enzyme, we might start to think about strategies to interfere with this defense mechanism of Mtb.Requirements: Applicants should have obtained a Master degree with a strong background and interest in protein biochemistry, structural biology and enzymology. Candidates are expected to have strong work ethics, excellent organization and communication skills, and critical thinking abilities. We offer a friendly, enthusiastic and interactive environment. Our staff is international and the working language is English. Please send a cover letter discussing your interests in the laboratory and the project as well as your CV and list of 3 individuals as references to joris.mess...@vib-vub.be.Kind regards,Inge Dr. Inge Van MolleVIB,Structural Biology Research CenterOxidative Stress SignallingStructural Biology BrusselsVrije Universiteit BrusselBuilding E, room 4.16,Pleinlaan 2,1050 Brussel,BelgiumTel. 003226291992Mobile 0032486521278
[ccp4bb] Postdoctoral position in structure-function studies of redox stress signaling proteins
On behalf of Prof. Joris Messens: Postdoctoral position in structure-function studies of redox stress signaling proteins Position: A postdoctoral Research position is immediately available for structure-function studies of plant proteins that control signaling during oxidative stress. Fellows will join an exciting research environment of the Messens VIB-laboratory in the Structural Biology Research Center in Brussels. The Messens laboratory is recognized as a world leader in the redox field, and the lab provides an outstanding position in protein biochemistry and structure, in a highly dynamic and team-oriented research group. Successful candidates will work on the FWO-project ‘The ROS-wave in plants: signaling along the sulfenome’ in collaboration with the Van Breusegem VIB-lab at Ugent, specialized in redox stress in plants. In this cutting-edge research environment of both labs, you will tackle essential biological problems in plant redox signaling. Project: In plants, reactive oxygen species (ROS) are accumulated during abiotic and biotic stress (drought, extreme temperatures and various pathogen attacks), leading to severe crop yield losses worldwide due to their adverse effect on plant growth and development. However, tightly regulated, ROS act as signal transducers orchestrating plant development and metabolic adaptation to stress conditions. To get insights into these processes, we recently identified the sulfenome of plant cells under oxidative (H2O2) stress. The sulfenome is the set of proteins in which a cysteine thiol (-SH) is oxidized to a sulfenic acid (-SOH). These reversible post-transcriptional modifications function as “thiol-switches” which alter the biochemical properties of redox sensing proteins. Together with the Van Breusegem lab, we identified redox active proteins involved in signal transduction, redox homeostasis and a plethora of other metabolic pathways in plants. In this project, we aim to establish a detailed structural and functional view of the mode of action of these redox proteins, in order to scrutinize their role in signaling during oxidative stress survival in plants. Requirements: Applicants should have obtained a PhD in the last 5 years. Expertise with protein biochemistry and structural biology is essential. Knowledge of biophysical techniques and enzymology is an asset. Please send a cover letter discussing your interests in the laboratory and the project as well as your CV and list of 3 individuals as references to joris.mess...@vib-vub.be. Dr. Inge Van Molle VIB, Department of Structural Biology Structural Biology Brussels, Vrije Universiteit Brussel Building E, room 4.16, Pleinlaan 2, 1050 Brussel, Belgium Tel. 003226291992 Mobile 0032486521278
[ccp4bb] number of reflections in XDSCONV output file
Dear all, I have a question regarding the number of reflections in the output file of XDSCONV, given a number of reflections in the input file. I have noticed that the number of reflections in the output file is only ~50% of the once accepted from the input file (ie the unique reflections)(input file is XSCALE.HKL or CORRECT_ASCII.HKL). This is in the case of FRIEDEL'S_LAW=FALSE: SPACE_GROUP_NUMBER= 91 UNIT_CELL_CONSTANTS=93.5793.57 364.05 90.000 90.000 90.000 FRIEDEL'S_LAW=FALSE MERGE=TRUE NUMBER OF REFLECTION RECORDS ON INPUT FILE 740375 NUMBER OF IGNORED REFLECTIONS (I -3.0*SIGMA)0 NUMBER OF REFLECTIONS ACCEPTED FROM INPUT FILE 106783 NUMBER OF UNIQUE REFLECTIONS ASSIGNED TO TEST SET 2864 NUMBER OF UNIQUE TEST REFLECTIONS INHERITED 0 NUMBER OF UNIQUE TEST REFLECTIONS NEWLY GENERATED 2864 NUMBER OF REFLECTION RECORDS ON OUTPUT FILE 57265 NUMBER OF RECORDS ASSIGNED TO WORKING SET54401 NUMBER OF RECORDS ASSIGNED TO TEST SET2864 In case FRIEDEL'S_LAW=TRUE, the number of unique reflections is just lower, and in the case the number of reflections in the output file does match the number of accepted reflections from the input file: SPACE_GROUP_NUMBER= 91 UNIT_CELL_CONSTANTS=93.5793.57 364.05 90.000 90.000 90.000 FRIEDEL'S_LAW=TRUE MERGE=TRUE NUMBER OF REFLECTION RECORDS ON INPUT FILE 740115 NUMBER OF IGNORED REFLECTIONS (I -3.0*SIGMA)0 NUMBER OF REFLECTIONS ACCEPTED FROM INPUT FILE 57244 NUMBER OF UNIQUE REFLECTIONS ASSIGNED TO TEST SET 2863 NUMBER OF UNIQUE TEST REFLECTIONS INHERITED 0 NUMBER OF UNIQUE TEST REFLECTIONS NEWLY GENERATED 2863 NUMBER OF REFLECTION RECORDS ON OUTPUT FILE 57244 NUMBER OF RECORDS ASSIGNED TO WORKING SET54381 NUMBER OF RECORDS ASSIGNED TO TEST SET2863 For some reason, the outcome of having Friedel's law false or true is thus the same. Can anyone explain this to me? A colleague and I checked whether she sees the same using PointlessScala to get mtz file, and this has the same effect. Kind regards, Inge Dr. Inge Van Molle Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW Tel 01223330190 iv...@cam.ac.uk
Re: [ccp4bb] Auto-Rickshaw: the EMBL-HH automated crystal structure determination platform
Being one of those succesgul users I can say that this is great news! Thanks Santosh, Inge -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Santosh Panjikar Sent: dinsdag 15 april 2008 9:45 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Auto-Rickshaw: the EMBL-HH automated crystal structure determination platform Dear Colleagues, Have you ever heard of Auto-Rickshaw? Auto-Rickshaw is the EMBL Hamburg automated structure determination platform, which is now available as a web service. Try it out and solve your structure in minutes. The EMBL-Hamburg beamline user have been successfully using this system for a little over three years. Now, for the new release with a lot of added functionalities, we are happy to announce that Auto-Rickshaw can be accessed by anybody in the Structural Biology community. The Auto-Rickshaw phasing protocols include SAD, SIRAS, MAD, MR and MRSAD. There are two versions: a beamline version and an advanced version. The beamline version is geared towards speed so as to deliver the results in the shortest amount of time whereas the advanced version can be used for more complete model building if the resolution of the data permits. For more detailed information visit http://www.embl-hamburg.de/Auto-Rickshaw The Auto-Rickshaw server is freely accessible to users who have the necessary software licences. Academic usage requires free of charge on-online registration at the same web site. Further inquiries can be made to Santosh Panjikar at [EMAIL PROTECTED] We would like to take this opportunity to thank all the developers of the various crystallographic programs for their kind permission to invoke their software within Auto-Rickshaw. We also gratefully acknowledge the feedback from the EMBL-Hamburg beamline users and everybody who provided test data. Santosh Panjikar on behalf of Auto-Rickshaw team Auto-Rickshaw team (Santosh Panjikar, Venkataraman Parthasarathy, Victor S. Lamzin, Manfred S. Weiss and Paul A. Tucker) Santosh Panjikar, Ph.D. [EMAIL PROTECTED] Staff Scientist EMBL Hamburg outstation http://www.embl-hamburg.de/~panjikar/ DESY, Notkestrasse 85Tel.:+49-40-89902-141 22603, Hamburg, Germany Fax: +49-40-89902-149
